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PR01450

Identifier
BKCHANNELB  [View Relations]  [View Alignment]  
Accession
PR01450
No. of Motifs
4
Creation Date
09-DEC-2000
Title
Calcium-activated BK potassium channel beta subunit signature
Database References
PRINTS; PR00169 KCHANNEL
Literature References
1. MILLER, C.
An overview of the potassium channel family.
GENOME BIOL. 1(4) 1-5 (2000).
 
2. ASHCROFT, F.M.
Ca2+ activated K+ channels.
IN ION CHANNELS AND DISEASE, ACADEMIC PRESS, 2000, PP.125-133.
 
3. KNAUS, H.G., FOLANDER, K., GARCIA-CALVO, M., GARCIA, M.L., KACZOROWSKI,
G.J., SMITH, M. AND SWANSON, R.
Primary sequence and immunological characterization of beta-subunit of high
conductance Ca2+-activated K+ channel from smooth muscle.
J.BIOL.CHEM. 269 17274-17278 (1994).
 
4. VERGARA, C., LATORRE, R., MARRION, N.V. AND ADELMAN, J.P.
Calcium-activated potassium channels.
CURR.OPIN.NEUROBIOL. 8(3) 321-329 (1998).
 
5. MCMANUS, O.B., HELMS, L.M., PALLANCK, L., GANETZKY, B., SWANSON, R. AND
LEONARD, R.J.
Functional role of the beta-subunit of high conductance calcium-activated
potassium channels.
NEURON 14 645-650 (1995).
 
6. NIMIGEAN, C.M. AND MAGLEBY, K.L.
The beta-subunit increases the Ca2+ sensitivity of large conductance Ca2+-
activated potassium channels by retaining the gating in the bursting states.
J.GEN.PHYSIOL. 113(3) 425-440 (1999).

Documentation
Potassium ion (K+) channels are a structurally diverse group of proteins
that facilitate the flow of K+ ions across cell membranes. They are
ubiquitous, being present in virtually all cell types. Activation of K+
channels tends to hyperpolarise cells, reducing the membrane's electrical
resistance, dampening nervous activity. In eukaryotic cells, K+ channels
are involved in neural signalling and generation of the cardiac rhythm, and
act as effectors in signal transduction pathways involving G protein-
coupled receptors (GPCRs). In prokaryotic cells, they play a role in the
maintenance of ionic homeostasis [1].
 
Structurally, calcium (Ca2+) activated channels belong to the subfamily of
K+ channels whose subunits contain 6 transmembrane (TM) domains: these are
the voltage-gated K+ (Kv) channels, the KCNQ channels, the EAG-like K+
channels and 3 kinds of Ca2+-activated K+ channel (BK, IK and SK) [2]. All
K+ channels share a characteristic sequence feature: a TMxTVGYG motif that
resides between the 2 C-terminal membrane-spanning helices, and forms 
the K+-selective pore domain [1].
 
Ca2+-activated K+ channels are a diverse group of channels that are
activated by an increase in intracellular Ca2+ concentration. They are
found in the majority of nerve cells, where they modulate cell excitability
and action potential. Three types of Ca2+-activated K+ channel have been
characterised, termed small-conductance (SK), intermediate conductance (IK)
and large conductance (BK) respectively [2-3].
 
BK channels (also referred to as maxi-K channels) are widely expressed 
in the body, being found in glandular tissue, smooth and skeletal muscle, 
as well as in neural tissues. They have been demonstrated to regulate 
arteriolar and airway diameter, and also neurotransmitter release. Each
channel complex is thought to be composed of 2 types of subunit: the pore-
forming (alpha) subunits and smaller accessory (beta) subunits.
 
The alpha subunit of the BK channel was initially thought to share the
characteristic 6TM organisation of the voltage-gated K+ channels. However,
the molecule is now thought to possess an additional TM domain, with an 
extracellular N-terminus and intracellular C-terminus. This C-terminal 
region contains 4 predominantly hydrophobic domains, which are also thought
to lie intracellularly. The extracellular N-terminus and the first TM region
are required for modulation by the beta subunit. The precise location of the
Ca2+-binding site that modulates channel activation remains unknown, but it
is thought to lie within the C-terminal hydrophobic domains.
 
The beta subunit (which is thought to possess 2 TM domains) increases the
Ca2+ sensitivity of the BK channel [5]. It does this by enhancing the time
spent by the channel in burst-like open states. However, it has little 
effect on the durations of closed intervals between bursts, or on the
numbers of open and closed states entered during gating [6].
 
BKCHANNELB is a 4-element fingerprint that provides a signature for the
calcium-activated BK potassium channel beta subunit. The fingerprint was 
derived from an initial alignment of 6 sequences: the motifs were drawn 
from conserved regions spanning virtually the full alignment length,
focusing on those sections that characterise the BK channel beta subunits
but distinguish them from other members of the K+ channel superfamily: motif
1 resides at the N-terminus, leading into the first putative TM domain;
motif 2 lies within the first TM domain; and motifs 3 and 4 reside within 
the linker region between the 2 TM domains. Two iterations on SPTR37_10f 
were required to reach convergence, at which point a true set comprising 11
sequences was identified.
Summary Information
11 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
411111111
30000
20000
1234
True Positives
CAKB_BOVIN    CAKB_CANFA    CAKB_COTJA    CAKB_HUMAN    
CAKB_RAT O35336 O35337 O35645
O46372 O88805 O93393
Sequence Titles
CAKB_BOVIN  CALCIUM-ACTIVATED POTASSIUM CHANNEL BETA SUBUNIT (MAXI K CHANNEL BETA SUBUNIT) (BK CHANNEL BETA SUBUNIT) (SLO-BETA) (K(VCA)BETA) (CHARYBDOTOXIN RECEPTOR BETA SUBUNIT) - BOS TAURUS (BOVINE). 
CAKB_CANFA CALCIUM-ACTIVATED POTASSIUM CHANNEL BETA SUBUNIT (MAXI K CHANNEL BETA SUBUNIT) (BK CHANNEL BETA SUBUNIT) (SLO-BETA) (K(VCA)BETA) - CANIS FAMILIARIS (DOG).
CAKB_COTJA PUTATIVE CALCIUM-ACTIVATED POTASSIUM CHANNEL BETA SUBUNIT - COTURNIX COTURNIX JAPONICA (JAPANESE QUAIL).
CAKB_HUMAN CALCIUM-ACTIVATED POTASSIUM CHANNEL BETA SUBUNIT (MAXI K CHANNEL BETA SUBUNIT) (BK CHANNEL BETA SUBUNIT) (SLO-BETA) (K(VCA)BETA) - HOMO SAPIENS (HUMAN).
CAKB_RAT CALCIUM-ACTIVATED POTASSIUM CHANNEL BETA SUBUNIT (MAXI K CHANNEL BETA SUBUNIT) (BK CHANNEL BETA SUBUNIT) (SLO-BETA) (K(VCA)BETA) - RATTUS NORVEGICUS (RAT).
O35336 MAXI POTASSIUM CHANNEL BETA SUBUNIT - MUS MUSCULUS (MOUSE).
O35337 MAXI POTASSIUM CHANNEL BETA SUBUNIT - RATTUS NORVEGICUS (RAT).
O35645 CALCIUM ACTIVATED POTASSIUM CHANNEL BETA SUBUNIT - MUS MUSCULUS (MOUSE).
O46372 LARGE CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL BETA SUBUNIT - ORYCTOLAGUS CUNICULUS (RABBIT).
O88805 CALCIUM ACTIVATED POTASSIUM CHANNEL BETA SUBUNIT SPLICED VARIANT - RATTUS NORVEGICUS (RAT).
O93393 PUTATIVE CALCIUM-ACTIVATED POTASSIUM CHANNEL REGULATORY SUBUNIT - GALLUS GALLUS (CHICKEN).
Scan History
SPTR37_10f 2  75   NSINGLE    
Initial Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
AQKRGEARALCLG CAKB_RAT 7 7 -
AQKRGETRALCLG CAKB_HUMAN 7 7 -
AQRRGETRALCLG CAKB_BOVIN 7 7 -
AQKRGETRALCLG O46372 8 8 -
AQKRGETRALCLG CAKB_COTJA 9 9 -
AQKRGETRALCLG O93393 9 9 -

Motif 2 width=14
Element Seqn Id St Int Rpt
GTTMLPLYQKSVWT CAKB_RAT 34 14 -
VTTVLPLYQKSVWT CAKB_HUMAN 34 14 -
GTTVLPLYQKSVWT CAKB_BOVIN 34 14 -
GTTMLPLYQKSVWT O46372 35 14 -
GITIVPFYTKSVWT CAKB_COTJA 36 14 -
GITIVPFYTKSVWT O93393 36 14 -

Motif 3 width=14
Element Seqn Id St Int Rpt
WVNVSAVGRWAVLY CAKB_RAT 77 29 -
WVNVSAAGRWAVLY CAKB_HUMAN 77 29 -
WVNVSSVGRWAVLY CAKB_BOVIN 77 29 -
WVNVSAVGKWAVLY O46372 78 29 -
WVNLTASGQEVMLY CAKB_COTJA 87 37 -
WVNLTASGQEVMLY O93393 87 37 -

Motif 4 width=15
Element Seqn Id St Int Rpt
TEDTRDQNQQCSYIP CAKB_RAT 92 1 -
TEDTRDQNQQCSYIP CAKB_HUMAN 92 1 -
TEDTRDQNHQCSYIP CAKB_BOVIN 92 1 -
TEETRDRNQQCSYIP O46372 93 1 -
TEDTLERNPKCSYVP CAKB_COTJA 102 1 -
TEDTLERNPKCSYVP O93393 102 1 -
Final Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
AQKRGETRALCLG O35337 8 8 -
AQKRGETRALCLG O88805 8 8 -
AQKRGETRALCLG O35645 8 8 -
AQKRGETRALCLG O35336 8 8 -
AQKRGETRALCLG CAKB_CANFA 7 7 -
AQKRGEARALCLG CAKB_RAT 7 7 -
AQKRGETRALCLG CAKB_HUMAN 7 7 -
AQRRGETRALCLG CAKB_BOVIN 7 7 -
AQKRGETRALCLG O46372 8 8 -
AQKRGETRALCLG CAKB_COTJA 9 9 -
AQKRGETRALCLG O93393 9 9 -

Motif 2 width=14
Element Seqn Id St Int Rpt
GTTVLPLYQKSVWT O35337 35 14 -
GTTVLPLYQKSVWT O88805 35 14 -
GTTVLPLYQKSVWT O35645 35 14 -
GTTVLPLYQKSVWT O35336 35 14 -
GTTMLPLYQKSVWT CAKB_CANFA 34 14 -
GTTMLPLYQKSVWT CAKB_RAT 34 14 -
VTTVLPLYQKSVWT CAKB_HUMAN 34 14 -
GTTVLPLYQKSVWT CAKB_BOVIN 34 14 -
GTTMLPLYQKSVWT O46372 35 14 -
GITIVPFYTKSVWT CAKB_COTJA 36 14 -
GITIVPFYTKSVWT O93393 36 14 -

Motif 3 width=14
Element Seqn Id St Int Rpt
WVNVSAVGRWAMLY O35337 78 29 -
WVNVSAVGRWAMLY O88805 78 29 -
WVNVSAVGRWAMLY O35645 78 29 -
WVNVSAVGRWAMLY O35336 78 29 -
WVNVSAVGRWAVLY CAKB_CANFA 77 29 -
WVNVSAVGRWAVLY CAKB_RAT 77 29 -
WVNVSAAGRWAVLY CAKB_HUMAN 77 29 -
WVNVSSVGRWAVLY CAKB_BOVIN 77 29 -
WVNVSAVGKWAVLY O46372 78 29 -
WVNLTASGQEVMLY CAKB_COTJA 87 37 -
WVNLTASGQEVMLY O93393 87 37 -

Motif 4 width=15
Element Seqn Id St Int Rpt
TEDTRDQNQQCSYIP O35337 93 1 -
TEDTRDQNQQCSYIP O88805 93 1 -
TEDTRDQNQQCSYIP O35645 93 1 -
AEDTRDQNQQCSYIP O35336 93 1 -
TEDTRDQNHQCSYIP CAKB_CANFA 92 1 -
TEDTRDQNQQCSYIP CAKB_RAT 92 1 -
TEDTRDQNQQCSYIP CAKB_HUMAN 92 1 -
TEDTRDQNHQCSYIP CAKB_BOVIN 92 1 -
TEETRDRNQQCSYIP O46372 93 1 -
TEDTLERNPKCSYVP CAKB_COTJA 102 1 -
TEDTLERNPKCSYVP O93393 102 1 -